Not a direct answer to the OP, but some comments on how things seem to work in general:
My base of proof is pretty small, but I've found my 3-4 is much more effective when I can mix in some Nickel, but of course there are teams that are pure 3-4 and are great and there are a couple that are pure nickel and are great. Same vein, I've found my Pro is much better if I can mix in some Trips. Have to decide how much time you want to put into formations, of course. Can't really do it halfway. And multiple formations can make recruiting tougher. Combining 3-4 with Nickel means you need both LB and DL in adequate numbers, but it's possible one group or the other won't get utilized enough during the season if scores dictate one or the other D.
To the mojolad question, when I go against teams that pass a lot to RB/TE I've found my Nickel D is more effective than my 3-4. I don't know if it's the extra DB or if I just have a better design in my nickel package.
Another way to affect how you do against certain O's or D's is deciding who you want to redshirt. If your primary D is 3-4 does it help to RS a DL? I know of at least two teams that seem to RS only O players and focus on trying to outscore the other guy, not worrying as much about D. Lots of interesting options that can affect how you play this game. I mostly only RS the highest potential, which is logical, but I'm thinking of changing to only D or only O to see if it makes a difference.